Korkosh Vyacheslav S, Zaytseva Anastasia K, Kostareva Anna A, Zhorov Boris S
Almazov National Medical Research Centre, St. Petersburg, Russia.
Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia.
Front Pharmacol. 2021 Nov 4;12:756415. doi: 10.3389/fphar.2021.756415. eCollection 2021.
Over 1,500 missense variants of sodium channel hNav1.5, which are reported in the ClinVar database, are associated with cardiac diseases. For most of the variants, the clinical significance is uncertain (VUS), not provided (NP), or has conflicting interpretations of pathogenicity (CIP). Reclassifying these variants as pathogenic/likely pathogenic (P/LP) variants is important for diagnosing genotyped patients. In our earlier work, several bioinformatics tools and paralogue annotation method consensually predicted that 74 VUS/NP/CIP variants of 54 wild type residues (set w54) are potentially damaging variants (PDVs). Atomic mechanisms underlying dysfunction of the PDVs are unknown. Here we employed a recent cryo-EM structure of the hNav1.5 channel with likely inactivated pore domain (PD) and activated voltage-sensing domains (VSDs), and models of the closed and open PD and resting VSDs to explore intersegment contacts of w54 residues. We found that 44 residues from set w54 contact 84 residues with 118 disease missense variants. These include 104 VUS/NP/CIP variants, most of which are associated with the loss-of-function Brugada syndrome (BrS1) or gain-of-function long QT syndrome (LQT3). Matrix representation of the PDVs and their contact variants facilitated recognition of coupled mutations associated with the same disease. In particular, BrS1-associated coupled mutations, which disturb the P-loops region with the selectivity filter slow inactivation gate, would cause the channel dysfunction. Other likely causes of the channel dysfunction include coupled BrS1-associated variants within VSDs that would destabilize their activated states and coupled LQT3-associated variants, which would stabilize the open PD or activated VSDs. Our study proposes mechanisms of channel dysfunction for scores of BrS1- and LQT3-associated variants, confirms status for 82% of PDVs, and suggests damaging status for their contact variants, which are currently categorized as VUS/NP/CIP variants.
临床变异数据库（ClinVar）中报告的超过1500种钠通道hNav1.5错义变体与心脏疾病相关。对于大多数变体而言，其临床意义尚不确定（VUS）、未提供（NP）或对致病性存在相互矛盾的解释（CIP）。将这些变体重新分类为致病/可能致病（P/LP）变体对于诊断基因分型患者很重要。在我们早期的工作中，几种生物信息学工具和旁系同源物注释方法一致预测，54个野生型残基（设定为w54）中的74个VUS/NP/CIP变体是潜在有害变体（PDV）。PDV功能障碍的原子机制尚不清楚。在此，我们采用了hNav1.5通道最近的冷冻电镜结构，其可能具有失活的孔结构域（PD）和激活的电压传感结构域（VSD），以及封闭和开放PD和静息VSD的模型，以探索w54残基的片段间接触。我们发现，w54组中的44个残基与84个残基接触，这些残基带有118个疾病错义变体。其中包括104个VUS/NP/CIP变体，其中大多数与功能丧失的 Brugada综合征（BrS1）或功能获得的长QT综合征（LQT3）相关。PDV及其接触变体的矩阵表示有助于识别与同一疾病相关的偶联突变。特别是，与BrS1相关的偶联突变会干扰带有选择性过滤器慢失活门的P环区域，从而导致通道功能障碍。通道功能障碍的其他可能原因包括VSD内与BrS1相关的偶联变体会破坏其激活状态，以及与LQT3相关的偶联变体，这会稳定开放的PD或激活的VSD。我们的研究提出了数十种与BrS1和LQT3相关变体的通道功能障碍机制，确认了82%的PDV状态，并暗示了其接触变体的有害状态，这些接触变体目前被归类为VUS/NP/CIP变体。
